Agent-based computational modeling of wounded epithelial cell monolayers

Computational modeling of biological systems, or ‘in silico biology’ is an emerging tool for understanding structure and order in biological tissues. Computational models of the behavior of epithelial cells in monolayer cell culture have been developed and used to predict the healing characteristics of scratch wounds made to urothelial cell cultures maintained in low and physiological [Ca2+] environments. Both computational models and in vitro experiments demonstrated that in low exogenous [Ca2+], the closure of 500mm scratch wounds was achieved primarily by cell migration into the denuded area. The wound healing rate in low (0.09mM) [Ca2+] was approximately twice as rapid as in physiological (2mM) [Ca2+]. Computational modeling predicted that in cell cultures that are actively proliferating, no increase in the fraction of cells in S-phase would be expected, and this conclusion was supported experimentally in vitro by BrdU incorporation assay. We have demonstrated that a simple rule-based model of cell behavior, incorporating rules relating to contact inhibition of proliferation and migration, is sufficient to qualitatively predict the calcium-dependent pattern of wound closure observed in vitro. Differences between the in vitro and in silico models suggest a role for wound-induced signaling events in urothelial cell cultures

White Dwarf Pollution by Asteroids from Secular Resonances

In the past few decades, observations have revealed signatures of metals polluting the atmospheres of white dwarfs. The diffusion time-scale for metals to sink from the atmosphere of a white dwarf is of the order of days for a hydrogen-dominated atmosphere. Thus, there must be a continuous supply of metal-rich material accreting onto these white dwarfs. We investigate the role of secular resonances that excite the eccentricity of asteroids allowing them to reach star-grazing orbits leading them to tidal disruption and the formation of a debris disc. Changes in the planetary system during the evolution of the star lead to a change in the location of secular resonances. In our Solar system, the engulfment of the Earth will cause the ν6 resonance to shift outwards which will force previously stable asteroids to undergo secular resonant perturbations. With analytic models and N-body simulations we show that secular resonances driven by two outer companions can provide a source of continuous pollution. Secular resonances are a viable mechanism for the pollution of white dwarfs in a variety of exoplanetary system architectures

Alignment of a circumbinary disc around an eccentric binary with application to KH 15D

We analyse the evolution of a mildly inclined circumbinary disc that orbits an eccentric orbit binary by means of smoother particle hydrodynamic (SPH) simulations and linear theory. We show that the alignment process of an initially misaligned circumbinary disc around an eccentric orbit binary is significantly different than around a circular orbit binary and involves tilt oscillations. The more eccentric the binary, the larger the tilt oscillations and the longer it takes to damp these oscillations. A circumbinary disc that is only mildly inclined may increase its inclination by a factor of a few before it moves towards alignment. The results of the SPH simulations agree well with those of linear theory. We investigate the properties of the circumbinary disc/ring around KH 15D. We determine disc properties based on the observational constraints imposed by the changing binary brightness. We find that the inclination is currently at a local minimum and will increase substantially before setting to coplanarity. In addition, the nodal precession is currently near its most rapid rate. The recent observations that show a reappearance of Star B impose constraints on the thickness of the layer of obscuring material. Our results suggest that disc solids have undergone substantial inward drift and settling towards to disc midplane. For disc masses $\sim 0.001 M_\odot$, our model indicates that the level of disc turbulence is low $\alpha \ll 0.001$. Another possibility is that the disc/ring contains little gas.Comment: 16 pages, 16 figures; accepted for publication in MNRA

Studies on nerve cells. I. The molluscan nerve cell, together with summaries of recent literature on the cytology of invertebrate nerve cells

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The Epitheliome: agent-based modelling of the social behaviour of cells

We have developed a new computational modelling paradigm for predicting the emergent behaviour resulting from the interaction of cells in epithelial tissue. As proof-of-concept, an agent-based model, in which there is a one-to-one correspondence between biological cells and software agents, has been coupled to a simple physical model. Behaviour of the computational model is compared with the growth characteristics of epithelial cells in monolayer culture, using growth media with low and physiological calcium concentrations. Results show a qualitative fit between the growth characteristics produced by the simulation and the in vitro cell models

Time-resolved measurements of black carbon light absorption enhancement in urban and near-urban locations of southern Ontario, Canada

In this study a photoacoustic spectrometer (PA), a laser-induced incandescence instrument system (LII) and an Aerosol Mass Spectrometer were operated in parallel for in-situ measurements of black carbon (BC) light absorption enhancement. Results of a thermodenuder experiment using ambient particles in Toronto are presented first to show that LII measurements of BC are not influenced by the presence of non-refractory material thus providing true atmospheric BC mass concentrations. In contrast, the PA response is enhanced when the non-refractory material is internally mixed with the BC particles. Through concurrent measurements using the LII and PA the specific absorption cross-section (SAC) can be quantified with high time resolution (1 min). Comparisons of ambient PA and LII measurements from four different locations (suburban Toronto; a street canyon with diesel bus traffic in Ottawa; adjacent to a commuter highway in Ottawa and; regional background air in and around Windsor, Ontario), show that different impacts from emission sources and/or atmospheric processes result in different particle light absorption enhancements and hence variations in the SAC. The diversity of measurements obtained, including those with the thermodenuder, demonstrated that it is possible to identify measurements where the presence of externally-mixed non-refractory particles obscures direct observation of the effect of coating material on the SAC, thus allowing this effect to be measured with more confidence. Depending upon the time and location of measurement (urban, rural, close to and within a lake breeze frontal zone), 30 min average SAC varies between 9 ± 2 and 43 ± 4 m<sup>2</sup> g<sup>−1</sup>. Causes of this variation, which were determined through the use of meteorological and gaseous measurements (CO, SO<sub>2</sub>, O<sub>3</sub>), include the particle emission source, airmass source region, the degree of atmospheric processing. Observations from this study also show that the active surface area of the BC aggregate, which is measured by the LII as the PPS, is an important parameter for inferring the degree of particle collapse of a BC particle. In addition, PPS could be a useful measurement for indicating the importance of recently emitted BC (e.g. from gasoline or diesel engines) relative to the total measured BC in the atmosphere